Secondary structure and small RNA-seq evidence for dme-mir-1011

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:16679012-16679095 - ATTCTGACCGTGCACGTGAGTTTTTGAGCCAGGAATAT--------AGTTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droSim1 chr3R:4780974-4781057 + ATTCTGACCGTGCACGTGAGTTTTTGAGCCAGGAATAT--------AGTTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droSec1 super_27:54817-54900 + ATTCTGACCGTGCACGTGAGTTTTTGAGCCAGGAATAT--------AGTTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droYak2 chr3R:5477803-5477886 - ATTCTGACCGTGCATGTGAGTTTTTGAGCCAGGAATAT--------AATTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droEre2 scaffold_4770:4975828-4975911 + ATTCTGACCGTCCACGTGAGTTTTTGAGCCATGAATAT--------AATTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droAna3 scaffold_13340:7952070-7952154 - GTGGTGACGGTGCATGTGAGTCTTTGAACCAGGAATAT--------AATTT----G-------TATATATTGGTTCAAATCGCTCGTAGAATCCTCCCTGGCAA
dp4 chr2:12756663-12756757 + ATTGTGACGATGCATGTGAGATTTTGAATCTAATATAT--------AATATAATCCGTACGTGTAT-ATATGGTTCAAATTACTCGTAGAACCCTCCCTGGCAA
droPer1 super_0:7702112-7702205 - ATTGTGACGATGCATGTGAGATTTTGAATCTAATATAT--------AATATAATCT-TACATGTAT-ATATGGTTCAAATAACTCGTAGAATCCTCCCTGGCAA
droWil1 scaffold_181108:2184466-2184552 + ATTCTGACCGTACATGTGAGTCTTTGAATCAGGAATAT--------ATTATCA--T-------TATATATTGGTTCGAAATGCTCGTAGAATCCACCTTGGCAA
droVir3 scaffold_13047:12031331-12031423 + ATTGTCACGGTGCATGTGAGTCATTGAACCAGGAATATATGTATGTAATTC----T-------TATATATTGGTTCAAATTTCTCGCAGAATCCGCCCTGGCAA
droMoj3 scaffold_6540:29750589-29750676 - ATTGTGACAGTGCATGTGAGTCTTTGAGCCAGGAATAT--------ATGTTCATCT-------TAT-TATTGGTTCAAATCTCTCGTAGAATCCTCCCTGGCAA
droGri2 scaffold_14830:1201859-1201943 + ATTGTCACTGAGCATGTGAGTCTTTGAGCCAGGAATAT--------AATTG----T-------TATATATTGGTTCAAACAACTCGTAGAATCCGCCCTGGCAA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:16679012-16679095 - ATTCTGACCGTGCACGTGAGTTTTTGAGCCAGGAATAT--------AGTTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droSim1 chr3R:4780974-4781057 + ATTCTGACCGTGCACGTGAGTTTTTGAGCCAGGAATAT--------AGTTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droSec1 super_27:54817-54900 + ATTCTGACCGTGCACGTGAGTTTTTGAGCCAGGAATAT--------AGTTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droYak2 chr3R:5477803-5477886 - ATTCTGACCGTGCATGTGAGTTTTTGAGCCAGGAATAT--------AATTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droEre2 scaffold_4770:4975828-4975911 + ATTCTGACCGTCCACGTGAGTTTTTGAGCCATGAATAT--------AATTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droAna3 scaffold_13340:7952070-7952154 - GTGGTGACGGTGCATGTGAGTCTTTGAACCAGGAATAT--------AATTT----G-------TATATATTGGTTCAAATCGCTCGTAGAATCCTCCCTGGCAA
dp4 chr2:12756663-12756757 + ATTGTGACGATGCATGTGAGATTTTGAATCTAATATAT--------AATATAATCCGTACGTGTAT-ATATGGTTCAAATTACTCGTAGAACCCTCCCTGGCAA
droPer1 super_0:7702112-7702205 - ATTGTGACGATGCATGTGAGATTTTGAATCTAATATAT--------AATATAATCT-TACATGTAT-ATATGGTTCAAATAACTCGTAGAATCCTCCCTGGCAA
droWil1 scaffold_181108:2184466-2184552 + ATTCTGACCGTACATGTGAGTCTTTGAATCAGGAATAT--------ATTATCA--T-------TATATATTGGTTCGAAATGCTCGTAGAATCCACCTTGGCAA
droVir3 scaffold_13047:12031331-12031423 + ATTGTCACGGTGCATGTGAGTCATTGAACCAGGAATATATGTATGTAATTC----T-------TATATATTGGTTCAAATTTCTCGCAGAATCCGCCCTGGCAA
droMoj3 scaffold_6540:29750589-29750676 - ATTGTGACAGTGCATGTGAGTCTTTGAGCCAGGAATAT--------ATGTTCATCT-------TAT-TATTGGTTCAAATCTCTCGTAGAATCCTCCCTGGCAA
droGri2 scaffold_14830:1201859-1201943 + ATTGTCACTGAGCATGTGAGTCTTTGAGCCAGGAATAT--------AATTG----T-------TATATATTGGTTCAAACAACTCGTAGAATCCGCCCTGGCAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ATTCTGACCGTGCACGTGAGTTTTTGAGCCAGGAATATAGTTCT-----------TATTATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAASizeHit CountTotal NormTotalGSM343915
Embryo
.........................................................TTATTGGTTCAAATCGCTCGCAG...............2313.0033
.........................................................TTATTGGTTCAAATCGCTCGCA................2211.0011
..........................................................TATTGGTTCAAATCGCTCGCAG...............2211.0011
dp4
ATTGTGACGATGCATGTGAGATTTTGAATCTAATATATAATATAATCCGTACGTGTATATATGGTTCAAATTACTCGTAGAACCCTCCCTGGCAASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-21.0 -20.6 -20.2

droSim1

-21.0 -20.6 -20.2

droSec1

-21.0 -20.6 -20.2

droYak2

-21.0 -20.6 -20.2

droEre2

-21.6

droAna3

-17.2 -16.6 -16.4

dp4

-12.3 -12.1 -11.7 -11.5

droPer1

-12.2 -12.1 -11.7 -11.7 -11.6 -11.5

droWil1

-14.9 -14.3

droVir3

-17.8 -17.7 -17.6 -17.3 -17.2 -17.1

droMoj3

-14.6 -14.4 -14.2 -14.0 -14.0 -13.9

droGri2

-17.3 -17.1 -16.7 -16.5

Generated: 01/05/2013 at 05:06 PM